2.1

Breaking Changes

• None, except the output .gff file is now gzipped

Non-breaking Changes

• writer task is now a Process (used to be a Thread)
  • the wgsim simulation is still a thread-based process
• reverted to calling wgsim.core() instead of as a subprocess (another possible speedup)
• longmoleculerecipe logic now writes a temp fasta file (speeds things along)
• N reads from a molecule are drawn from exponential distribution instead of lognormal and then transformed out of log
  • the log-unlog transformations were slowing things down significantly
• Set a minimum of 2 reads from a molecule prior to possible downgrade to singleton
  • more reliable singleton ratios

Fixes

• simplified thread-watching and backpressure
• should have hopefully addressed some of the noticeable slowdown between v1 and v2